From 16S rRNA-gene sequencing of cow RUMEN microbiome samples: - 6 treatments for rumen samples + ruminal liquid (base) + (“AE1”,“AE sintético 1”,“Carvacrol”, “p-cymene”, “γ-terpinene”, “no treatment (ruminal liquid + diet)”)
Between-sample variability from 16S rRna-gene sequencing data.
## Warning in as.dist.default(matx): non-square matrix
## Warning in x[row(x) > col(x)] <- d^2: number of items to replace is not a
## multiple of replacement length
Clustering by treatment (PCA): after removing samples from treatment no treatment (ruminal liquid + diet) # BECAUSE WE KNOW THAT THERE WE SHOULD NOT HAVE DIFFERENCES BETWEEN GROUPS
## Warning in metaMDS(matx0, k = 3): stress is (nearly) zero: you may have
## insufficient data
Clustering by type (MDS): NMDS2 vs NMDS3
Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.
Below the ANOVA table from the model:
\[ X = \mu + treatment + + treatment*type + e \]
| Df | SumsOfSqs | MeanSqs | F.Model | R2 | Pr(>F) | |
|---|---|---|---|---|---|---|
| treatment | 6 | 0.1670642 | 0.027844 | 1.361631 | 0.1536547 | 0.203 |
| residuals | 45 | 0.9202063 | 0.020449 | NA | 0.8463453 | NA |
| total | 51 | 1.0872705 | NA | NA | 1.0000000 | NA |
## Square root transformation
## Wisconsin double standardization
## Run 0 stress 0.005866665
## Run 1 stress 0.002880717
## ... New best solution
## ... Procrustes: rmse 0.04570152 max resid 0.1011523
## Run 2 stress 0.002993376
## ... Procrustes: rmse 0.01197886 max resid 0.0252612
## Run 3 stress 0.004457099
## Run 4 stress 0.008358046
## Run 5 stress 0.002991392
## ... Procrustes: rmse 0.02118136 max resid 0.04484306
## Run 6 stress 0.004604658
## Run 7 stress 0.002968823
## ... Procrustes: rmse 0.02073788 max resid 0.04566674
## Run 8 stress 0.002156464
## ... New best solution
## ... Procrustes: rmse 0.01458369 max resid 0.0336482
## Run 9 stress 0.006683282
## Run 10 stress 0.001652964
## ... New best solution
## ... Procrustes: rmse 0.01260981 max resid 0.02825254
## Run 11 stress 0.0007457592
## ... New best solution
## ... Procrustes: rmse 0.006741449 max resid 0.01520747
## Run 12 stress 0.008546079
## Run 13 stress 0.008932748
## Run 14 stress 0.002043376
## Run 15 stress 0.0005669045
## ... New best solution
## ... Procrustes: rmse 0.00227706 max resid 0.004998075
## ... Similar to previous best
## Run 16 stress 0.001146092
## Run 17 stress 0.001468972
## Run 18 stress 0.001723621
## Run 19 stress 0.0002764154
## ... New best solution
## ... Procrustes: rmse 0.003813089 max resid 0.008499326
## ... Similar to previous best
## Run 20 stress 0.006475395
## *** Solution reached